Related papers: Black-White Array: A New Data Structure for Dynami…
This paper introduces the batch-parallel Compressed Packed Memory Array (CPMA), a compressed, dynamic, ordered set data structure based on the Packed Memory Array (PMA). Traditionally, batch-parallel sets are built on pointer-based data…
The "ordered set" abstract data type with operations "insert", "erase", "find", "min", "max", "next" and "prev" is ubiquitous in computer science. It is usually implemented with red-black trees, $B$-trees, or $B^+$-trees. We present our…
Data-structure dynamization is a general approach for making static data structures dynamic. It is used extensively in geometric settings and in the guise of so-called merge (or compaction) policies in big-data databases such as Google…
Real-world data sets often exhibit temporal dynamics characterized by evolving data distributions. Disregarding this phenomenon, commonly referred to as concept drift, can significantly diminish a model's predictive accuracy. Furthermore,…
Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost…
We present linear-space data structures for several frequency queries on trees, namely: path mode, path least frequent element, and path $\alpha$-minority queries. We present the first linear-space data structures, requiring $O(n…
Motivated by an application in computational topology, we consider a novel variant of the problem of efficiently maintaining dynamic rooted trees. This variant requires merging two paths in a single operation. In contrast to the standard…
It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the…
The dynamic trees problem is to maintain a tree under edge updates while supporting queries like connectivity queries or path queries. Despite the first data structure for this fundamental problem -- the link-cut tree -- being invented 40…
Accurate wide area network (WAN) bandwidth (BW) is essential for geo-distributed data analytics (GDA) systems to make optimal decisions such as data and task placement to improve performance. Existing GDA systems, however, measure WAN BW…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…
Understanding how a learned black box works is of crucial interest for the future of Machine Learning. In this paper, we pioneer the question of the global interpretability of learned black box models that assign numerical values to…
The \emph{Order-Maintenance} (OM) data structure maintains a total order list of items for insertions, deletions, and comparisons. As a basic data structure, OM has many applications, such as maintaining the topological order, core numbers,…
Comparing data defined over space and time is notoriously hard, because it involves quantifying both spatial and temporal variability, while at the same time taking into account the chronological structure of data. Dynamic Time Warping…
Machine Learning requires a large amount of training data in order to build accurate models. Sometimes the data arrives over time, requiring significant storage space and recalculating the model to account for the new data. On-line learning…
This paper describes the most efficient way to manage operations on ranges of elements within an ordered set. The goal is to improve existing solutions, by optimizing the average-case time complexity and getting rid of heavy multiplicative…
The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several area in science and…
The Burrows-Wheeler Transform (BWT) is an efficient invertible text transformation algorithm with the properties of tending to group identical characters together in a run, and enabling search of the text. This transformation has extensive…
The Positional Burrows--Wheeler Transform (PBWT) is a data structure designed for efficiently representing and querying large collections of sequences, such as haplotype panels in genomics. Forward and backward stepping operations --…
Symbolic data structures for model checking timed systems have been subject to a significant research, with Difference Bound Matrices (DBMs) still being the preferred data structure in several mature verification tools. In comparison,…